Teenage Mutant Ninja Turtles: Mutagen Chains
by Crimson-Eyes26
Summary: AU story for the Teenage Mutant Ninja Turtles. Fate has a funny way of interfering with people's lives. See how fate plays out for a group of brothers, a lab assistant, a vigilante who attracts trouble, a girl seeking to escape the past, and the evil forces at work to destroy them. What happens when fate brings them together? Rated T but may change later on.
1. Manhattan, the City of Beginnings

**Author's Note: Wow, it's been a while since I wrote a Ninja Turtles story, hasn't it? Well, I wanted to give something a try. I've made an AU that combines elements from the other incarnations and wanted to write about it. This AU is called Mutagen Chains, and this chapter is just an introductory to some of the primary characters. Other key characters you'll see in the next few chapters. There are a few OCs and some pairings but the pairings won't come until later on. Enough of my babbling, so enjoy!**

* * *

Chapter 1: Manhattan, the City of Beginnings

_We interrupt this program to bring you this special news alert. It seems as though an unknown group of vigilantes have decided to deal with the growing gang threat in Manhattan themselves. Amid the increasing complaints about gang activities and lack of police action, members of the notorious street gang the Purple Dragons have been found beaten and tied up in an alleyway. The gang members were taken into police custody, but not before proclaiming being attacked by 'green men'. Who are these mystery fighters? Are they the new city heroes? Or are they a bigger threat than the local gangs? More info to come on this story! For Channel 6 News, this is Irma Langinstein, signing off!_

The news report echoed off the HD televisions on display in the electronic store window, drawing attention from a few but others simply passing by as they were totally oblivious. A pair of green eyes, however, locked onto the screen and listened intently to the report. It wasn't the notion of 'green men' that interested the individual, but rather the notion that someone was finally standing up to the gangs, especially the Purple Dragons. Whoever had the guts to do that was either very brave or very reckless. The person the eyes belonged to, a redheaded woman, gripped the strap on her purse tighter until the news broadcast ended.

April O'Neil wasn't exactly the type of person to be interested in the news, especially when it concerned vigilantes. Most of the time, her mind was set on what her job of the day would be over at Stockgen, whether it be testing out odd robots or injecting poor animals with drugs to see how it would benefit humans. She didn't know what to make of Baxter Stockman or his questionable methodologies concerning technology and biotechnology, but she knew she needed the paycheck. While vigilantes were the last thing on her mind, something about this group of them struck her curiosity. She stared so intently at the TV screens she didn't even notice a police car pulling up to the nearby station and coming to a stop.

Two officers stepped out of the car and opened up the back door, pulling out a man in his mid-to-late twenties after some struggle. The cuffed man blew some of his wild black hair out of his face and glared at the police officers as though they conspired to do this to him. He growled, exposing his teeth and some of those he lost he lost from his days as a high school hockey player.

"Do we really have to go through this again, Jones?" The first officer asked in an annoyed tone. "How many times have we told you to stop takin' the law in your own hands?"

Casey Jones spat and stared at the policemen with even more contempt. "I would if ya chumps would just do ya job! What, do th' Dragons have you guys in their pockets or somethin'!?"

"Ah, shut up Jones!" The second officer snorted, smacking him on the back with a little too much force. "We actually deal wit' the Dragons! They just don't show up much is all!"

April overheard this and had a hard time believing that statement. The Purple Dragons were out all the time, and the police often chose not to deal with them. Along with the Dragons, she heard people often complain of people dressed in red and black stalking the streets like ghosts. Some people claimed they were in fact phantoms…others said they were assassins. Whatever they were, they still made people afraid to walk the streets at night. With her job, she couldn't afford not to go out at night. A buzz reverberated through her purse and she pulled it out to see what caused it; more than likely it was a text.

Fifteen minutes or you'll have your pay docked.

"Typical of you, Mr. Stockman…" April muttered in a low voice. She placed her smartphone back into the purse and went about her way to Stockgen. She didn't want to end up like that guy who accused Stockman of animal cruelty over seventeen years ago…whatever happened to that guy? She only knew of the rumors of him, and learning that Stockman would punish employees for the littlest things. He could actually be more brutal than a Purple Dragon. Well, unless she wanted to run into one or a green man, she had to hurry, so she began to sprint down the street to get to the lab.

* * *

**_Apartment for Rent. Payment to be discussed. Please speak to Akane Murasama, landlord, if interested._**

That's what the newspaper clip read as a pair of teal eyes scanned the bold letters. New York was a long way from home, but she couldn't help where new job opportunities led her, especially when you worked in the medical field. So now the brunette found herself in a taxi cab with a few suitcases riding to a studio apartment building. Her mother practically begged her not to go, as New York was supposedly dangerous, but she was a big girl and could take care of herself. The vehicle suddenly came to a stop and the young woman handed the cabbie the amount of cash needed before stepping out.

This was a new start for Cheyloe Doggett, or Chey as her friends knew her. A new start from the past, a chance to be on her own and be fully independent. She stared from the newspaper clipping to the apartment building, a sigh escaping her lips as she picked up her suitcases and walked inside. The sun was setting, and she hoped the landlord wasn't out early. She managed to get into the door despite the many suitcases, stopping for a moment to see a redheaded girl dashing down the street as if she were running for her life.

"Hello?" Cheyloe called out, getting inside and peering into the front office. "Um, I'm looking for a Ms. Murasama. I'm the new tenant; we talked the other day."

"That would be me."

Cheyloe turned around and saw a woman approach her. She appeared to be of Japanese descent but had short red hair and wore a beautiful dress; she believed it was a yukata. She had her arms crossed as she approached, but she seemed to have a warm smile. "I am Akane Murasama. You must be Cheyloe Doggett. I welcome you."

"Thank you, ma'am." The brunette replied warmly, though exhaustion due to travel hinted in her tone. "Sorry for sounding tired. I've traveled through at least five or six states to get here. So, where am I to stay?"

Akane chuckled and led her to an elevator, pressing the up button and encouraging her to get on. "You'll be on the fourth floor. These are all studio apartments, and if you have any furniture with you, I'll put it in place of the furniture currently in your apartment."

Cheyloe shook her head. "Oh no, ma'am. All I have are some clothes and a few personal belongings. Any furniture in there is fine."

The elevator came to a stop and the landlord smiled. "Fair enough. We'll discuss payment once we get inside. I do hope that you'll like it."

Chey figured she would like it regardless, and she followed Akane without a word to the apartment that was intended to be hers for as long as she chose or could afford to stay. The landlord stuck the key into the lock, gave it a few quick turns, and opened the door. The brunette examined the apartment and felt her eyes light up. It looked beautiful, not too big yet not too small, and it had a pleasant smell. She sat down her suitcases to take a better look at the place, taking in the scents of flowering plants in the space.

"This place…this place is great!" The brunette wore a huge grin and the tone of her voice was clearly bounding with energy. "I think I'm going to love it here!"

Akane nodded and smiled back at her, the younger woman's optimism apparently contagious. "Your payment is four-hundred and fifty a month plus utilities. If it's too high, I'll lower it."

Chey thought about the money she recently received from a close friend, an amount that would be enough to cover a year's worth of rent. Of course, she still intended to work over at the memorial hospital, though the extra cash would help greatly. "Oh, no, it's fine. With my income, it should leave enough for groceries."

"Sounds good." The landlord decided. "Please…let me know if you need anything at all, Ms. Doggett."

* * *

_"__In other news, Stockgen founder and head scientist Baxter Stockman has a proposal to deal with the rising rat problem in Manhattan. The proposal involves a robotic solution known as the MOUSER project for the cleanup, but local animal activist groups blast Stockman, claiming the proposal to be 'inhumane'."_

The light from the outdated flat screen flickered onto the faces of the two viewers, the bright white hue mixing with the green darkened by the lack of illumination anywhere else in the room. Of course, living underground didn't provide much natural light at all, and while the smell, which could best be described as garbage mixed with portable toilet waste, was something displeasing to normal noses, they had to live in it for over seventeen years; you could say they went 'nose-blind' to it. The two viewers paid attention to the newscast until one, sporting a red headband, groaned and shot up from his seat.

"This is a waste. Who cares 'bout some stupid robot project, anyway?" He asked, not expecting anyone to answer.

"Raph, have a little more appreciation for robotics." The other viewer sporting purple reprimanded, staring at him with irritation before going back to the television. "I mean, one of these days, robots will be replacements for training dummies and give YOU a better workout."

Raphael snorted and breathed out of his nose, fogging up the metal nose ring he had. "A robot wouldn't be good enough ta give me a workout, Donnie. Besides, other than heating up food or lettin' us watch TV, what're they good for?"

Donatello cocked an eye ridge. "Seriously? Robots actually operate on people to keep them from dying, and they build those motorcycles you like so much." He placed his chin in his hands and stared back at the news report. "But something's bothering me about this. We haven't seen a lot of rats down here, not enough to cause problems topside. So why would they even need them?"

Raphael and Donatello were two out of four brothers, who would live average lives if they could if it weren't for one problem. That problem was, simply, that they were mutants. Mutant turtles to be exact. They knew they started out as ordinary pet turtles over seventeen years ago until they were doused by a mysterious green goo and became what they are now. The broken canister that the goo came in stood as sort of a trophy mounted on the wall of their home…which was of course in the sewers of Manhattan. Raphael was the second-youngest of the bunch while Donatello was the second-oldest. They didn't live by themselves, of course. They had their father, whom they affectionately called Splinter. However, Splinter seemed to be keeping a closer eye on them lately, and it was because they were coming of age to the point they wouldn't be kids anymore.

A loud POP suddenly echoed behind them, and the two turtles almost jumped mid-air to get away from the noise. It wasn't but just seconds later that an audible snicker followed, causing Raph and Donnie to glare behind the old sofa at the source. A turtle sporting orange glanced up at them innocently with blue eyes.

"Mikey!" Raphael snarled. "Didn't I tell ya **not** ta get in my firecracker stash!?"

Michelangelo, the youngest out of the four turtles, shrugged as though he did nothing wrong. "I can't remember when you told me. Did you tell Master Splinter that you **have** a firecracker stash?"

The red-banded turtle immediately roared and went to chase after the orange-banded turtle. "Just don't eveh get in it again or I'm gonna knock yer block off BIG TIME!"

"Not my fault you suck at finding hiding places for your stuff!" Mikey retorted, his tongue poking through the cleft in his upper lip. "You should find a better spot for those magazines with those hot chicks you hide from Splinter!"

"You found those too!?" Raph roared, ready to wrap his hands around his baby brother's neck in retaliation.

"Would you two knock it off!?" A stern voice boomed. "Your seventeen years old and you're both acting like a pair of bratty toddlers!"

That's when the two young brothers stopped when in walked none-other than Leonardo, the eldest of the turtles sporting a blue headband. Since he was the eldest of the brothers, he was made the leader of them, though he would never speak against his father's authority. However, despite being the eldest, many would not assume that automatically if they compared the heights of the brothers. Donatello was the tallest, followed by Raphael, then Leonardo, and Michelangelo, but Leo and Mikey were almost the same height.

"Tch." Raphael grunted before stepping away from Michelangelo, shooting a heated glare at his elder brother. "What would you know about bratty toddlers, Pigeon Toes?"

"Raph, would you please stop calling me that?" Leo griped, rolling his deep blue eyes. "That was long ago; I don't do that anymore, just like you apparently don't hold your breath when you don't get your way, or am I wrong?"

"You tryin' ta imply somethin', **Fearless **Leader?" Raphael asked the blue-banded turtle, danger clearly in his tone. "Are ya? Cuz if ya wanna start somethin' ya can't finish, I'd be more than happy ta-"

"HEY GUYS!" Mikey suddenly cut in, his finger jabbing wildly at the TV. "Check out that girl next to the science dude!"

The turtles all stared at the television, which still aired the news report; it must have been more of a news conference than a simple report. They took notice of the young redheaded woman next to Baxter Stockman, the one who seemed to be nervous standing in the background seemingly tinkering with one of the robots intended for use. They seemed to stare in complete awe, though Raphael quickly walked away.

"Aw, where ya goin' Raphie?" Michelangelo asked with a pout on his face. "Don't you wanna watch more of the chick?"

Raph turned back to his siblings and gritted his teeth. "She's a human, Mikey. What good have humans done for us? Nothin'…they could care less about freaks like us, and they'll NEVER care."

As Raphael went back to his room, Michelangelo stared forlornly at his other brothers, sitting down on the sofa and wrapping his arms around his knees. "Leo...how come Raph has ta act like that, huh? What did humans ever do ta him?"

Leonardo sighed and sat down next to his brother, patting his shell to give him some sort of comfort. "...That's just how Raph is, unfortunately. Maybe one day, just one day...we'll get to walk around topside without having to worry about people screaming at us or trying to hurt us. But for now...let's just focus on getting along and living comfortably down here."


	2. Chance Encounter

**Author's Note: Okay, I finally finished Chapter 2. We see more insight on the turtles but this is a focus on the meeting of April O'Neil, even though the turtles have been spotted somewhat by our new arrival. A face-to-face meeting with her will be in the next couple of chapters, and we'll be seeing Splinter and more of Casey Jones and the bad guys. Okay, here we go!**

* * *

Chapter 2: Chance Encounter

Everything seemed quiet. Even the sounds of water running through the tunnels disappeared into silence as Leonardo breathed out and deepened the concentration of his meditation. Meditation…everyone had a way to steady their nerves, and this was his. He did it the most out of the four brothers, a technique he picked up from their father, and he was the best at it. Donatello's mind was always racing, so he couldn't empty it to concentrate and relax. Raphael was too tense and too impatient to meditate; he often blew it off as a waste of time. Michelangelo's mind was everywhere, so he couldn't make himself focus on the subject at hand…that and laziness played into it. Leonardo had a balanced mind fit for meditation, something required for the art of ninjitsu.

Ninjitsu. It was something else their father passed down to them. They practiced it since they were mere toddlers, and now they were almost masters at it. Of course, that would take even more years of practice and building up of their skills. Until then, they still had much to learn. Like with meditation, Leo was the best student at it, often making Raph jealous. If Raph would just stop with his petty jealousy, he would be better at it…at least that's what Leo formulated. But the others often wondered if Leo began to get arrogant with his skill, and it seemed he always had to be in the right. Even Splinter feared that this would be so…

"Leo!" The voice of Michelangelo whispered as a finger poked him in the cheek. "Leeeeeooooo!"

The blue-banded turtle cracked open his bluish-grey eyes to glance at his baby brother, a frown on his lips. "Mikey, what is it? I'm in the middle of meditation, if you can't clearly see that."

Mikey snickered and flashed a grin. "Leo, yer just a stick in th' mud. I guess you don't wanna go topside with us."

Leo's eyes widened at the word 'topside'. "Topside!? Master Splinter said we're forbidden from going up there, in case you forgot! Let me guess, this is Raph's idea?"

"Nah, it was mine this time." The orange-banded turtle stated without missing a beat. "I found this leftover pizza from a local pizzeria, and it's the best I've ever eaten, dude! I was gonna go get some more, but I can't do it alone! I told Raph we should go up and he said yeah, so did Donnie!"

Leonardo shoved his face into his palm before getting up. He immediately knew that there was no deterring his brother from carrying out his little plan; not even threatening to tell Sensei would change his mind. Well, if he couldn't stop them, he had to at least make sure they stayed out of trouble and made sure they came back before their father noticed. With a deep sigh, he stared at Mikey and muttered, "If we're going, someone has to keep an eye on you three…and that someone HAS to be me. And we're taking the rooftops so no one can see us, got it?"

Mikey grinned and instantly gave him a playful punch on the shoulder. "Yer the best, Leo! I'll give you some extra pizza! Let's go!"

Leo rolled his eyes and rubbed his shoulder before following Mikey to the sewer tunnel that led to the topside, where Raph and Donnie waited for them. Hopefully, they would go get the stupid pizza and get home unnoticed. Maybe something wouldn't go wrong tonight…maybe. He kept walking with his baby brother until the middle brothers came into view underneath a manhole cover and ladder.

"I didn't think you were able to convince him Mikey…but it looks like you did." Donatello examined in surprise.

Raphael snorted and chewed on his lip for a moment before growling out in impatience. "Enough marvelin' over Mikey havin' charm, Donnie. Let's just get up there and go! I'm tired of waitin'!"

* * *

"No, Anna, I'm not lonely up here. I'm serious! Ms. Muramasa is an awesome landlord! I know it's just been a couple of days but I know she's a trustworthy lady!"

Cheyloe walked around with a cell phone to her ear, glancing out the window of her apartment every few minutes to get a good view of the city surrounding her. She had been in her apartment for two days and already felt at ease in her new home. Now she spent the evening having a telephone conversation with her best friend states away trying to convince her she was one-hundred-percent fine. Why wouldn't she be?

"Look, Anna, you don't have to worry about me all the time, okay?" Chey assured in exasperation. "I'm doing okay here. My job is going great and the traffic's not as bad as I thought it would be, so just-"

She suddenly stopped when her eyes went back to the window and the city view. It was right then that her line of vision caught something that wasn't there before. Chey walked closer to the window, moving her long bangs out of the way of her right eye, and saw four silhouettes on the rooftops, highlighted by the illumination of the moon. The silhouettes ran rapidly on the rooftops, and it was clear to the young woman they weren't normal…in fact, they didn't appear human. She stared at them as though the very sight put her in a trance, and she ignored her friend repeating her name in order to get her to reply for a moment.

"Anna…I'll call you back, okay?" Chey murmured before hanging up the phone and continuing to stare outside. Whatever those things were, they had her attention. She remembered reading a newspaper article one morning about mysterious vigilante sightings. Could this be them? Or could it be with past events she was finally crazy enough to be seeing hallucinations? She remembered a note that came with the money to help with rent that was in the handwriting of her closest confidant.

_Get better._

"I certainly hope I can get better." Cheyloe mumbled in a whisper.

* * *

"O'Neil!" A disgruntled voice called to the redhead hovering over a high-powered microscope. "Stockman must be playing favorites with the youth these days!"

April lifted her head from the scope and turned to face the middle-aged man complaining about the 'young people'. Professor Harold Lilija worked for Baxter Stockman for close to twenty years, when April was just a toddler. She always heard the man to be of a brilliant mind and sharp intellect, but it was often overlooked in favor of his eccentricity. April had to admit, the man was odd, and he had a strange vocabulary, spewing out nonsensical and often considered made-up words such as 'obstruse'. When she first started working at Stockgen after college, he would often pick on her until she happened to mention her dad's name. Apparently, Kirby O'Neil was famous amongst the employees of Stockgen.

"And why is it you say that, Mr. Lilija?" April asked innocently, flipping her curly hair out of her eyes.

"How many times have I told you to just call me Harold?" Lilija muttered, rolling his eyes behind his glasses. "Stockman just gave me a pink slip! I've worked for the man for twenty years, spilling so much blood, sweat, and tears, and THIS is the way he repays me!?"

April's eyes widened. "Mr. Stockman fired you? But you're his best scientist!"

"That's what I said! But does that rat of a man ever listen? Of course not!" Lilija ranted. "All because I told him this MOUSER project was a waste! There's not even a single rat on the streets, yet he wants to build those ugly things to get rid of an imaginary problem!"

Now April was confused. "What do you mean 'imaginary problem'? You mean he built the MOUSERS for nothing?" She suddenly thought about it, not noticing her now-former coworker leaving. "Wait…what if he built them for something else and just used the rat problem story as a cover. But what else could they be used for?"

The redhead glanced at the computer on the nearby table, which had numerous files on projects that dated back to maybe ten years ago secured within the hard drive. There were some files that were highly-classified and could only be seen by Baxter Stockman himself. It would get her into trouble if she happened to glance through the classified files; it was possible the MOUSER project fell into that category. But she was great at computer hacking. After all, back in high school, she always managed to get around the security blocking certain music sites. Who's to say she couldn't do it again, this time for laboratory projects?

Dashing over to the keyboard, she typed her way into the archives and searched, scrolling down through an almost-endless supply of documents until she came across one called MOUSER. She clicked on it and, to her surprise, it wasn't exactly classified. She opened it up and it of course brought up the schematics of the small robot. It was then April noticed something in the list of documents that stood out. It was titled 'TCRI INFILTRATION'. Wasn't TCRI some sort of multimillion dollar company specializing in things similar to Stockgen? Why would Stockman want to infiltrate TCRI?

"Is this…is this what the MOUSERS are really for?" April whispered to herself. "These things aren't for a pest problem…they're for a corporate break-in!"

"I'm surprised you would figure that out, Miss O'Neil."

April abruptly turned around in her seat and saw none-other than Baxter Stockman glowering at her. She had to admit, she now felt afraid and felt her heart pounding out of her chest. But if there's one thing she wouldn't do, it was cower down. The redhead got up from her seat and stared at her boss. "Mr. Stockman, why did you lie to the people about the purpose of the project? Why do you want to break into TCRI!?"

Stockman snorted, his mustache rising with his following sneer. "Why should a lowly employee have a right to know that?" He began to walk around the table, April noticing he had a remote in his hand. "I will admit April, I did have respect for your father. Kirby was a brilliant man, always wanting to reach higher. But he was too much of a stickler for the rules. He wasn't willing to obliterate the competition." He began to grit his teeth after the word 'competition'. "My laboratory was the best around…until TCRI showed up ten years ago and began cutting into my profits. So what do I do to get rid of the problem?"

April stepped back when Stockman stalked closer, patting her hand on the desk to find something she could use as a weapon to defend herself. The man decided to continue. "All I have to do is gather a few MOUSERS into TCRI and…BOOM."

"You're going to use the MOUSERS to blow up TCRI!?" April spat. "That's crazy, Stockman! The police can trace them back to you! There's no way you'd get away with it!"

"Au contraire, Miss O'Neil." Stockman smirked. "I designed the MOUSERS so that once they detonate, they completely disintegrate and leave no trace whatsoever." His smirk faded and he stared at April, who then noticed the sound of mechanical footsteps slowly approaching from behind the man. "But there is one thing I have to take care of first…anyone who knows about my plan shall be…taken out of the picture."

April watched in horror as the small mechanical robots, the MOUSERS she helped build and bring to life, marching towards her with sharp, snapping jaws. They tested the robots and she knew they had enough power in those jaws to snap through human flesh and bone…and now they were programmed to attack her, the now-primary threat to Stockman's agenda. The redhead glanced between the MOUSERS and the exit door that led to the rooftop. But the rooftop was a dead-end…what was she going to do? She would half to think about it when she got there, and she wasted no time in jumping up on the desks and tables to avoid the robotic army of jaws and make it to the door and to the stairs.

* * *

"Mikey, did you really have to place an order for FIVE pizzas?" Leonardo griped, watching his baby brother carry five steaming cardboard boxes of the hot pies. "We barely had enough money to cover them, and calling an order for them put us at risk for being exposed!"

Michelangelo seemed to wave the entire thing off, licking his lips at the fantasy of sinking his teeth into hot cheese, tomato sauce, and pepperoni. "Leo, ya like that Zen stuff, right? So how come you don't act all Zen around us, huh? Chillax, bro! We're goin' home!"

"I'd have to agree with Mikey, Leo." Donatello interjected, trying to suppress a snicker. "Maybe it's time you started practicing what you preach in terms of being **calm**."

Raphael snorted and rolled his eyes before walking ahead of his brothers. He knew this was a stunt Mikey pulled off before; actually calling the pizzeria, placing an order, and having the delivery boy leave it at an undisclosed location for pickup. He was always able to afford it with money they collected that happened to fall down the storm drain. Still, he wouldn't be caught doing it himself because it meant a human coming near him. He wouldn't admit exactly how much he resented them, though no one could figure out why he resented them in the first place. He was about to be the first to get to the fire escape when the sounds of a door slamming open, a scream, and metallic snapping hit his ears.

"What on earth was that?" Donnie questioned as he jerked his head around for the source of the noise.

Mikey suddenly pointed his finger to an adjacent building. "Hey guys, look! It's that chick from the news report the other day!"

The turtles ran to the edge of the rooftop to see if Mikey's claim was true. Sure enough, there was the redheaded woman from the conference running to the edge of the rooftop being chased by odd mechanical gremlins. She glanced over the edge and looked like she was about to contemplate jumping off just to escape.

"Dudes, we gotta help 'er!" The orange-banded turtle put the pizzas down and pulled out the nunchaku in his belt. "If we don't, she's gonna get hurt?"

"Why should we help 'er Mikey?" The red-banded turtle snorted. "She's a human! We don't need ta get involved!"

"So you're just in for letting her die?" The purple-banded turtle spat in disbelief. "That goes against everything Sensei taught us!"

The blue-banded turtle narrowed his eyes and pulled out his trusty katana blades. "If you're going to complain Raph, you can sit this one out. The rest of us are going to give her help, human or not." He pointed the tip of his blade to the rooftop. "All right boys, let's go!"

Raph stared at his brothers leaving to play hero sputtering and holding his hands out. He clenched them into fists and stood almost pouting for a moment. He thought about what Donnie said about his proclamation going against everything they were taught…that all life was precious. And then he thought about how their Sensei would react if he heard he was about to leave a woman to die. Groaning in defeat, he pulled out his sais and rushed after his brothers.


	3. Meet the Mutants

**Author's Note: I do apologize for the lack of updates, I've had writer's block and classes. But anyway, now April finally meets the Turtles and we get to meet Splinter. And let me tell you, he has a surprising connection with both April and Stockgen. Next, what will the Turtles and April do to stop Baxter's plans for TCRI? When will we see more of Casey and our new friend Cheyloe? And what's with the reports of ninjas in New York? Stay tuned and find out!**

* * *

Chapter 3: Meet the Mutants

April forced herself to keep from screaming as she pressed her back against the ledge of the rooftop. The MOUSERS marched closer, their footsteps noisily clanging against the asphalt-laced roof towards their panicking target, full intention of ripping her to shreds. Why did she have to be such a snoop? Why did she have the audacity to open those files and discover the dirt on Stockman? Sure, what he was planning to do with the robots was absolutely wrong, but was it really worth risking her life and getting herself killed in a few moments? She didn't want to seem like a damsel in distress, but it wouldn't hurt to be rescued by somebody, ANYBODY, right now!

Just when all hope seemed lost for April O'Neil…that's when she saw the tip of a sharp blade penetrate the head of one of the MOUSERS.

The redhead gasped silently, her eyes tracing the blade up to the hilt, the handle, and the hand holding it. The hand was green, bandaged…and had three fingers. Her eyes proceeded to lock onto the wielder of the sword…wait, giant humanoid turtles weren't supposed to exist, were they? They were just about as real as alligators in the sewers, right? She suddenly saw the sword-wielding turtle about to get overwhelmed by the other MOUSERS swarming in. That is, until another turtle jumped into the fray and whacked the robots with a long staff. Another one wielding nunchucks swooped in and bashed many of the MOUSERS in their heads.

"How many of these things are there!?" Leonardo asked, slicing through another robot.

Donatello bashed his own set of MOUSERS before deciding to answer that. "Enough for a small army! Just watch for those jaws! From the looks of the designs, they could tear your limbs off!"

"Thanks fer the info, Donnie!" Raphael growled, impaling one of the mechanical gremlins with the tip of his sai with brutal force. "Tell us somethin' we DON'T know!"

"Oh, shut up, Raph!" Donnie retorted. He saw a robot head straight for his red-banded brother's head and promptly whacked it away before it could bite into his flesh and skull. "You're welcome!"

April watched in silence as the creatures fought her employer's creations. Well, maybe now she could say ex-employer. Okay, first she discovers her boss wants to blow up a rival company, then he sends MOUSERS to come and kill her, and now she was being saved by humanoid reptiles? It was apparently enough to literally blow her mind, as she proceeded to pass out from the shock of it all. It was a shame she didn't get to see the very last machine destroyed by the orange-banded turtle.

"Hey guys!" Michelangelo addressed his brothers, pointing to the redhead's fainted form. "She passed out! What're we gonna do with her!?"

"Well, we obviously can't take her to a hospital." Donatello admitted, letting out an exasperated sigh. "If the emergency room staff saw four grown turtles bring an unconscious woman to their doors, we can certainly look forward to the government tracking us down."

Leonardo mulled over the situation, avoiding the glances of his brothers. If they left the woman here, then whoever was trying to harm her would more than likely come to finish her off. And there was no way for them to know where she lived; it would risk them being seen. There was one option left…but that would mean having to tell Sensei that they snuck out and fought; just the thought of their father being angry gave him goose bumps. But what choice did they have, really? Sheathing his swords, he looked his brothers in the eyes and decided, "We have to bring her back to the lair."

Needless to say, Raphael was the first to disagree. "Leo, are you crazy!? Yer wantin' ta bring a HUMAN to th' lair!? It ain't happenin'!"

"Raph, it's the only thing we can do!" Leo retorted. "I don't like it either, but if we don't, then whoever was trying to kill her will come to do the job themselves!"

"But-"

"Remember what Sensei told us…ALL life is precious. That includes hers." The blue-banded turtle gave his final argument before commanding, "Donnie, help me carry her."

"All right! We're takin' her home wit' us!" Mikey cheered, pumping his fists in the air.

Raph stared at his brothers, completely dumbfounded. Shock wearing off, his lips quickly curled into a sneer and his hands quickly clenched into fists. How could Leo be so stupid? How could he just flat-out decide they were bringing a human woman into their home, where she could potentially tell all her friends-if she had any-about their lair? Then it wouldn't be long until they were on the 6 o'clock news! But he would keep it in for now…and if Sensei caught them and their new 'pet', he would open his mouth and not mince words.

* * *

April groaned, squeezing her eyes shut and scowling as her consciousness came back. Was everything that happened before just some terrible nightmare? Had she still been in her apartment and asleep the entire time? But this didn't feel like her bed…and it certainly didn't smell like her bed. Trying to ignore the stale sewage smell coming from whatever she was sleeping on, she opened her eyes and saw that she was not in her apartment. The ceiling seemed of metal and concrete, and she saw pipes running through along with a few tunnels overhead. And that's when she heard voices.

"Dude, I think she's waking up." One voice whispered.

"What exactly are we going to do with her?" Another murmured.

"Once she comes to, we can talk that out with her, now let her have some air." A third commanded.

"Talk with 'er, yeah, after we make sure she keeps 'er mouth shut." The final voice growled.

The redhead sat up from her resting place, an old sofa, and focused her vision. And there they were…the four humanoid turtles that saved her from the MOUSERS. All of the stared at her as though she were a circus freak show exhibit; why they weren't in one was a mystery to her. She took a moment to look at them before she took in a deep breath and let out a scream. Once she screamed, the ones in orange and purple screamed along with her. The one in red smacked them on the back of their heads before walking up to her and glowering down, causing her to become silent.

"W…W-What's going on…?" April stuttered, still fearful. "W-W-Where am I?"

"Ma'am…calm down, please." Leonardo requested, putting his hands up. "We don't want to wake our father. We rescued you from the robots trying to harm you."

"Robots…" April repeated, clearly confused. "Wait, you…you mean the MOUSERS." She suddenly forgot about the MOUSERS and focused her attention back on them. "Just…what are you? What happened to Stockman?"

"Stockman?" Donatello repeated, his face immediately lighting up. "Do you mean Dr. Baxter Stockman? Weren't those his creations? What would cause the robots he created to attack you? Nothing about this makes-"

"What is going on in here!?"

Everyone in the room immediately snapped their mouths shut, Donatello being the first, at the sound of the booming voice. April noticed the turtles starting to tremble in fear or anticipation, but who was the source of the voice and why were they afraid? She got her answer when she saw a figure emerge from one of the pipes laying overhead. The figure jumped down and landed in front of them, causing the turtles to flinch. First humanoid turtles…now a humanoid RAT? She laid her eyes upon said-humanoid rat, who stood several inches taller than her and had a long, braided beard and whiskers forming together into a mustache. The creature wore a long, faded robe and walked with a cane, and it was walking dangerously towards the turtles.

"S-Sensei, we can explain!" Donnie spoke, holding his hands in front of his face.

Mikey nodded feverishly. "Yeah Dad! We had no choice but to bring her here! She was-"

Before he could say more, the rat-man, their Sensei, took his cane and swiftly whacked all of them on their calves and ankles, making them all cry out in pain and bounce on their feet, Donnie and Raph falling down. April jumped back at the hits, and she felt sorry for them. It was then the rat-man turned his attention to her. At the sight of her, his eyes softened ever so slightly. His eyes then went back to the turtles. "What have I told you about going to the surface!? You know it is a dangerous place, and now you've brought a human here!"

"Sensei, we had no choice!" Leonardo dared to object, causing his Sensei's head to whip towards him. "If we didn't save her, she would've died! She was attacked by those robots made by Baxter Stockman!"

At that name, the rat-man froze, and he took another look at April. His brown eyes studied her much more carefully, and he reached a clawed hand to the redhead, making her flinch. His claws gently brushed the skin around her eyes, eyes that brought nostalgia. "You…you look so much like Dr. O'Neil…"

April gasped. "How…how do you know my dad?"

The rat-man leaned on his cane, not paying attention to the turtles getting to their feet. "Now I remember…I haven't seen you since you were a small child. All of the animals liked you just about as much as they liked me."

The redhead sat back as memories from her childhood came flooding back. She remembered coming to Stockgen a few times while her father still worked there, and she met Baxter along with Harold Lilija. There was also another man she met there…the one who cared for the test-subject animals. He was a man of Japanese descent, and seemed cheerful. He even let her feed some of the rats used for testing. It was then his voice was familiar to her…but what happened to him. "…Mr. Yoshi?"

Mikey stared at his Sensei as though he grew another head. "Dad, she knows you?"

The rat slowly nodded his head. "That is correct…but I go by the name Splinter now. I suppose you're wondering why I look like this. Well…it is a long story." He turned to the turtles and spoke softly, "My sons…you may want to sit down. It is time you heard the entire story as well."

The turtles nodded and went to sit around the sofa, though Raphael was the last to do so. Splinter got into a kneeling position on a nearby cushion and put his cane to the side. He stroked at his beard and whiskers before taking a deep breath and collecting his memories. "As you know, I came from an area in Yakushima, Japan. However…Ms. O'Neil does not know that I am part of a clan that is more than likely long-gone now…the Hamato Clan. My family comes from a long line of the practitioners ofNinjitsu…and with every clan, there are feuds. One clan in particular…we were embroiled in a long blood-feud…the Foot Clan. However, not all in the Foot were enemies…one member in particular, we developed a secret friendship I thought would break the chains of the past. His name…was Oroku Saki."

"Are you two…still friends?" April asked quietly.

"It would have been that way…but everything changed when we met a girl by the name of Tang Shen." Splinter sighed. "Shen was raised by a Japanese family, but it was obvious that she was of Chinese descent. Saki did not care for anyone of Chinese descent…but it didn't matter to me where she hailed from. You couldn't have met a more beautiful and compassionate woman. She was the one who gave me the nickname Splinter…after she saw me splitting boards to impress her."

Mikey snickered at that, but stopped when their Sensei continued. "After marrying Shen…my friendship with Saki grew strained. At the same time…he found secrets within his diminished clan…and became enveloped in a darkness that had to have come from the Devil himself. I came home from teaching pupils one day…and I found Shen cold and dead on the floor. Saki was there waiting…and we fought bitterly until my home was set ablaze by followers he recruited from the outside. He believed I perished…but I escaped and came to America…to New York. To this day…I have never figured out why he would kill her, other than for his dislike of her Chinese blood."

April brought her knees to her chest and wrapped her arms around them. She noticed the turtles bowing their heads in sadness, having to hear the tale of their Sensei's heartbreak. Despite the tears prickling his eyes, Splinter continued with his story.

"Work was hard to find, but I managed to earn a job as a caretaker for the animals at Stockgen. It was there I met Dr. Baxter Stockman…and your father, Dr. Kirby O'Neil. Kirby was a kind and morally-rigid man…Baxter Stockman is a man I never cared for due to his indifference towards people and animals. It was over seventeen years ago that I cared for a newly-hatched clutch of turtles…four in all that made it. I also developed a bond with the rats. It was during that time I witnessed Stockman's cruelty towards the animals…some he even willingly tortured. I can honestly say your father was in the dark about the abuse. I could not stand by and watch his harsh treatment towards the turtles. I grabbed the rats and let them loose before gathering the turtles and attempting to take them home with me."

"…What happened?" The redhead questioned, having an idea where the story was going.

Splinter closed his eyes before opening them to look at her. "Stockman got wind of me taking the animals…and he threw a canister of an odd substance he experimented with at me as I reached the back door. The canister shattered and covered myself and the turtles with a glowing green ooze. When we finally escaped…I watched in horror as I slowly lost my human form…and took on the characteristics of a rat. At that same moment…I had dropped the turtles…and they began to take on the characteristics of a human. They grew to the size of human infants…they cried out, confused about what was happening. I had no choice but to gather them and flee where no one would look for us…the sewers."

April stood frozen before looking at the turtles surrounding her. Those turtles Yoshi rescued from Stockgen…they were the same turtles who saved her from the MOUSERS…saved her from Stockman. She wanted to say something but let the rat continue. "The turtles began to show they could talk, and later walk. As they grew, I knew they needed to find a way to protect themselves, should something happen that they venture to the surface. If they went up without being prepared, they would be ridiculed…attacked…taken to places like Stockgen and experimented on. So…I decided to pass my heritage of Ninjitsu onto them. They excelled quickly…but they don't know all of my skills just yet. Before making the sewers our home, I collected some things from my home…one of them being a book Shen cherished…a book on Renaissance art. It was there that I found names for the turtles…my sons."

The four turtles suddenly stood up and stared back and forth at April and Splinter. The latter took the moment to introduce them to the redhead, starting with the blue-banded one. "Leonardo, my eldest son and the master of the katana." He moved to the purple-banded one. "Donatello…a boy of great intellect, and master of Bojutsu." Then it was the red-banded one's turn. "Raphael, a fighter of passionate fury and master of the sai." Finally, he got to the orange-banded one. "Michelangelo…my youngest son and master of the nunchaku."

The turtles proceeded to bow in front of her, but not before Mikey could sneak a wink at her. That earned him an elbow to the side from Raph. April bowed her head slightly out of respect, still stunned by the tale she heard. So the one thing they had in common was Baxter Stockman…wait…she now remembered Baxter's plans concerning TCRI…was he still going to carry it out? He didn't know whether or not she was still alive, so maybe she could find a way to stop him before it was too late. "Stockman…he's planning on using the MOUSERS to attack TCRI."

"You can't be serious!" Donatello shouted. "Why would Stockman want to go after TCRI!? Corporate espionage or something!?"

"More like corporate destruction." The redhead muttered. "He's planning on using the MOUSERS to blow up TCRI…and they're programmed to explode and leave no trace. I need to find a way to get back there and reprogram them…then Stockman can't use them…but I need to get in there unnoticed. Question is…how?"

The turtles looked around silently before three pairs of eyes landed on Donnie. Donnie blinked in surprise before he let out a chuckle. "Well, who else would it be? Leave that to me, Ms. O'Neil."

"Please…call me April." She replied, wearing a small smile.


End file.
